Understanding the Conserved Domain Search
 
 

Click on the image to see full-size!		 Go back to the "formatting BLAST" page and click on the "IGc" icon, the "Conserved Domain Search" screen should appear - as shown by the thumbnail to the left. The largest bit score - and the lowest p value - is shown by the arrow.

Click on this link.

 

Click on the image to see full-size!		 The "Conserved Domain Search" screen contains two important links:
  1. The "Show Structure" button, which will launch a 3-D visualization of the IGc domain in Cn3D (the NCBI molecule viewer).

    2.  
  2. The "Pfam" link, which goes to a portal providing access to protein and domain families.
In this tutorial we will follow the "Structure" link first, and the "Pfam" link second.

Click on the "Structure" button.
A dialog box appears: Select "Open with Cn3D (default)" and click "OK".

Click on the image to see full-size!		 A new window will open which depicts the IGc domain. 

Select the following menu options, as shown in the thumbnail to the left: 
Style --> Rendering shortcuts --> Tubes

The image which is shown to the left is colored to show the secondary structures (such as b pleated sheet, a helix and random coil). Figure out how this was done.

How does the "Sequence/Alignment Viewer" correspond to the image?

  • What happens when you highlight a few amino acids in the 1MHE_A sequence?
  • What happens when you double-click on an amino acid in the structure?
This structure can be viewed from any perspective in 3 dimensions, by holding down the left key and moving the mouse!
  • X = roll.
  • Y = yaw (pointing left or right).
  • Z = pitch (pointing up or down).
Position the structure as shown in the full-size image above.

Click on the image to see full-size!		 Return to the window "Conserved Domain Search" window, as shown to the left.

Click on the "Pfam" link.
A new screen appears which looks like the thumbnail below.

Click on the image to see full-size!		 This screen provides a very useful overview of the proteins and domains which are members of the family. 

Included in this are links to PubMed for a deeper literature review of the subject.

Click on the image to see full-size!		 Scroll down to the 2 x 2 matrix which is shown in the thumbnail to the left, which provide 4 important sources of information. In this tutorial, we will follow two of them:
  1. Domain Organization
  2. Phylogenetic Tree
Select "View 11 representative architectures", and click on "View Graphic".

Click on the image to see full-size!
A conserved domain is a recurring sequence pattern or motif which occurs within a larger sequence. It has a characteristic structure and function, and in concert with other domains, determines the function of the entire protein. Before you proceed with this section be certain that you REVIEW and understand the importance and functionality of 
which was discussed earlier!

This Pfam screen shows the variety of sequences which contain the IGc conserved domain. 

Click on the  button to see all of the sequences in a particular architectural group. For example, details of each of the 7 sequences in the MHC-1, MHC-1, c1 set  group can be viewed, with links to their GenBank records.

 
NOTE: Do not worry about the details of structure and function of each domain unless your Instructor spends time on a deep exposition of it. What is really important is an appreciation of the modular nature of domains. 

In this case, the IGc domain can be deployed in a variety of different ways to produce Immunoglobulin molecules with different immune activities!

Click on the image to see full-size!		 Return to the 2 x 2 matrix as shown in the thumbnail to the left. 

Select "Full", and click on "ATV Applet".
 

Click on the image to see full-size!		 The link goes to a phylogenetic tree, as shown in the thumbnail to the left. This may be thought of as an evolutionary lineage based on the similarity of IGc sequences in humans and other organisms. Important points are:
  • the small squares are called "nodes" and indicate putative evolutionary ancestors.
  • the length of the lines indicates evolutionary distance.
  • the black mess is actually composed of all the species names. The screen contains so much data however, that they appear on top of each other.

Click on the image to see full-size!		 Click on the search menu (circled in pink in the thumbnail). Type "sheep" in the search box which appears, and click on "OK".

Text which contains the word "sheep" will now appear in red as shown.
 

Click on the image to see full-size!		 Make the data viewable by clicking on:
  • "Zoom in Y" to spread the text vertically.
  • Zoom in X" to shorten the tree horizontally.
When this is done, it can be seen that the IGc domain occurs in a number of different sequences throughout the sheep genome. Moreover it also has very similar relatives in cows (BOVIN, BOS), humans (PONPY), pigs, E. coli (TRASP), white-bellied spider monkey (ATEBE), HIV (sagoe) - even a dung beetle (BUBBU)!
Top of Page
 

Back to "Sequence similarity searching using NCBI BLAST"

Back to "Index for ENTREZ and Data Base Searches"

RETURN TO SITE MAP